Milo w complex design

library(MouseGastrulationData)

Registered S3 methods overwritten by 'htmltools':
  method               from         
  print.html           tools:rstudio
  print.shiny.tag      tools:rstudio
  print.shiny.tag.list tools:rstudio

Load gastrulation atlas data

embryo_sce <- EmbryoAtlasData(type="processed")
yes

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snapshotDate(): 2020-04-27
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource

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see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
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loading from cache

embryo_sce

class: SingleCellExperiment 
dim: 29452 139331 
metadata(0):
assays(1): counts
rownames(29452): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742
rowData names(2): ENSEMBL SYMBOL
colnames(139331): cell_1 cell_2 ... cell_139330 cell_139331
colData names(17): cell barcode ... colour sizeFactor
reducedDimNames(2): pca.corrected umap
altExpNames(0):

Preprocessing

hvgs

   [1] "ENSMUSG00000052217" "ENSMUSG00000010760" "ENSMUSG00000055609" "ENSMUSG00000061808" "ENSMUSG00000032083" "ENSMUSG00000095180"
   [7] "ENSMUSG00000002985" "ENSMUSG00000024990" "ENSMUSG00000069919" "ENSMUSG00000024406" "ENSMUSG00000024391" "ENSMUSG00000020644"
  [13] "ENSMUSG00000023043" "ENSMUSG00000052187" "ENSMUSG00000051159" "ENSMUSG00000051855" "ENSMUSG00000031765" "ENSMUSG00000025491"
  [19] "ENSMUSG00000027562" "ENSMUSG00000000805" "ENSMUSG00000069917" "ENSMUSG00000047751" "ENSMUSG00000021728" "ENSMUSG00000000031"
  [25] "ENSMUSG00000024503" "ENSMUSG00000007872" "ENSMUSG00000003153" "ENSMUSG00000072235" "ENSMUSG00000021477" "ENSMUSG00000027478"
  [31] "ENSMUSG00000032494" "ENSMUSG00000021268" "ENSMUSG00000025351" "ENSMUSG00000023906" "ENSMUSG00000049382" "ENSMUSG00000000184"
  [37] "ENSMUSG00000086503" "ENSMUSG00000050071" "ENSMUSG00000028773" "ENSMUSG00000079523" "ENSMUSG00000047139" "ENSMUSG00000032291"
  [43] "ENSMUSG00000102252" "ENSMUSG00000032359" "ENSMUSG00000047844" "ENSMUSG00000021190" "ENSMUSG00000049775" "ENSMUSG00000042745"
  [49] "ENSMUSG00000064357" "ENSMUSG00000025068" "ENSMUSG00000070436" "ENSMUSG00000039323" "ENSMUSG00000037664" "ENSMUSG00000022150"
  [55] "ENSMUSG00000045394" "ENSMUSG00000021278" "ENSMUSG00000018339" "ENSMUSG00000031762" "ENSMUSG00000027239" "ENSMUSG00000004885"
  [61] "ENSMUSG00000031827" "ENSMUSG00000064358" "ENSMUSG00000040204" "ENSMUSG00000024661" "ENSMUSG00000092341" "ENSMUSG00000051257"
  [67] "ENSMUSG00000031633" "ENSMUSG00000037335" "ENSMUSG00000064341" "ENSMUSG00000060591" "ENSMUSG00000064370" "ENSMUSG00000030246"
  [73] "ENSMUSG00000064351" "ENSMUSG00000039910" "ENSMUSG00000029838" "ENSMUSG00000005892" "ENSMUSG00000021939" "ENSMUSG00000046402"
  [79] "ENSMUSG00000020469" "ENSMUSG00000001403" "ENSMUSG00000006519" "ENSMUSG00000085696" "ENSMUSG00000031155" "ENSMUSG00000030544"
  [85] "ENSMUSG00000064363" "ENSMUSG00000047945" "ENSMUSG00000041959" "ENSMUSG00000042684" "ENSMUSG00000064354" "ENSMUSG00000028691"
  [91] "ENSMUSG00000016256" "ENSMUSG00000024619" "ENSMUSG00000068220" "ENSMUSG00000029622" "ENSMUSG00000028645" "ENSMUSG00000021765"
  [97] "ENSMUSG00000027533" "ENSMUSG00000070803" "ENSMUSG00000051579" "ENSMUSG00000025219" "ENSMUSG00000018217" "ENSMUSG00000018593"
 [103] "ENSMUSG00000048450" "ENSMUSG00000026728" "ENSMUSG00000020733" "ENSMUSG00000042712" "ENSMUSG00000064345" "ENSMUSG00000028832"
 [109] "ENSMUSG00000043501" "ENSMUSG00000029646" "ENSMUSG00000032366" "ENSMUSG00000032698" "ENSMUSG00000040856" "ENSMUSG00000020186"
 [115] "ENSMUSG00000046432" "ENSMUSG00000006356" "ENSMUSG00000042750" "ENSMUSG00000030560" "ENSMUSG00000018569" "ENSMUSG00000049422"
 [121] "ENSMUSG00000024987" "ENSMUSG00000020205" "ENSMUSG00000050777" "ENSMUSG00000062327" "ENSMUSG00000020407" "ENSMUSG00000032080"
 [127] "ENSMUSG00000025161" "ENSMUSG00000026547" "ENSMUSG00000040808" "ENSMUSG00000028194" "ENSMUSG00000050732" "ENSMUSG00000028484"
 [133] "ENSMUSG00000035783" "ENSMUSG00000040466" "ENSMUSG00000001666" "ENSMUSG00000064373" "ENSMUSG00000075706" "ENSMUSG00000026688"
 [139] "ENSMUSG00000076441" "ENSMUSG00000052305" "ENSMUSG00000004665" "ENSMUSG00000017723" "ENSMUSG00000041126" "ENSMUSG00000055653"
 [145] "ENSMUSG00000046550" "ENSMUSG00000094777" "ENSMUSG00000005681" "ENSMUSG00000033379" "ENSMUSG00000060143" "ENSMUSG00000001827"
 [151] "ENSMUSG00000032902" "ENSMUSG00000021591" "ENSMUSG00000031883" "ENSMUSG00000030342" "ENSMUSG00000029922" "ENSMUSG00000031297"
 [157] "ENSMUSG00000015937" "ENSMUSG00000032387" "ENSMUSG00000042367" "ENSMUSG00000079641" "ENSMUSG00000052397" "ENSMUSG00000019880"
 [163] "ENSMUSG00000034165" "ENSMUSG00000045763" "ENSMUSG00000031383" "ENSMUSG00000028536" "ENSMUSG00000076431" "ENSMUSG00000036030"
 [169] "ENSMUSG00000067786" "ENSMUSG00000054932" "ENSMUSG00000024232" "ENSMUSG00000056758" "ENSMUSG00000030934" "ENSMUSG00000066652"
 [175] "ENSMUSG00000020086" "ENSMUSG00000096210" "ENSMUSG00000030796" "ENSMUSG00000090125" "ENSMUSG00000019851" "ENSMUSG00000007041"
 [181] "ENSMUSG00000030654" "ENSMUSG00000032249" "ENSMUSG00000020098" "ENSMUSG00000027186" "ENSMUSG00000027523" "ENSMUSG00000075304"
 [187] "ENSMUSG00000070858" "ENSMUSG00000026864" "ENSMUSG00000062997" "ENSMUSG00000039329" "ENSMUSG00000029581" "ENSMUSG00000044080"
 [193] "ENSMUSG00000074227" "ENSMUSG00000029103" "ENSMUSG00000040699" "ENSMUSG00000015217" "ENSMUSG00000020649" "ENSMUSG00000027447"
 [199] "ENSMUSG00000027712" "ENSMUSG00000078350" "ENSMUSG00000038526" "ENSMUSG00000021361" "ENSMUSG00000029580" "ENSMUSG00000018362"
 [205] "ENSMUSG00000020048" "ENSMUSG00000039221" "ENSMUSG00000070348" "ENSMUSG00000029446" "ENSMUSG00000017493" "ENSMUSG00000041431"
 [211] "ENSMUSG00000020577" "ENSMUSG00000020911" "ENSMUSG00000053931" "ENSMUSG00000026726" "ENSMUSG00000020609" "ENSMUSG00000006378"
 [217] "ENSMUSG00000063524" "ENSMUSG00000027907" "ENSMUSG00000009646" "ENSMUSG00000031799" "ENSMUSG00000071708" "ENSMUSG00000069662"
 [223] "ENSMUSG00000072944" "ENSMUSG00000032946" "ENSMUSG00000026193" "ENSMUSG00000026970" "ENSMUSG00000032892" "ENSMUSG00000019804"
 [229] "ENSMUSG00000049932" "ENSMUSG00000047281" "ENSMUSG00000027510" "ENSMUSG00000031434" "ENSMUSG00000020027" "ENSMUSG00000032446"
 [235] "ENSMUSG00000022257" "ENSMUSG00000006442" "ENSMUSG00000024538" "ENSMUSG00000028307" "ENSMUSG00000002265" "ENSMUSG00000006311"
 [241] "ENSMUSG00000031074" "ENSMUSG00000019942" "ENSMUSG00000046727" "ENSMUSG00000062170" "ENSMUSG00000056209" "ENSMUSG00000092035"
 [247] "ENSMUSG00000058135" "ENSMUSG00000001642" "ENSMUSG00000040564" "ENSMUSG00000026576" "ENSMUSG00000044221" "ENSMUSG00000031146"
 [253] "ENSMUSG00000006589" "ENSMUSG00000021953" "ENSMUSG00000003955" "ENSMUSG00000042812" "ENSMUSG00000001473" "ENSMUSG00000047557"
 [259] "ENSMUSG00000029761" "ENSMUSG00000031490" "ENSMUSG00000019998" "ENSMUSG00000063856" "ENSMUSG00000068614" "ENSMUSG00000036402"
 [265] "ENSMUSG00000030762" "ENSMUSG00000034349" "ENSMUSG00000025902" "ENSMUSG00000021102" "ENSMUSG00000020737" "ENSMUSG00000039218"
 [271] "ENSMUSG00000020766" "ENSMUSG00000004897" "ENSMUSG00000011114" "ENSMUSG00000067377" "ENSMUSG00000042106" "ENSMUSG00000021453"
 [277] "ENSMUSG00000032050" "ENSMUSG00000004951" "ENSMUSG00000022742" "ENSMUSG00000052396" "ENSMUSG00000031438" "ENSMUSG00000032126"
 [283] "ENSMUSG00000019987" "ENSMUSG00000075588" "ENSMUSG00000068079" "ENSMUSG00000026605" "ENSMUSG00000037169" "ENSMUSG00000061086"
 [289] "ENSMUSG00000005161" "ENSMUSG00000021835" "ENSMUSG00000001270" "ENSMUSG00000029844" "ENSMUSG00000032562" "ENSMUSG00000031326"
 [295] "ENSMUSG00000018666" "ENSMUSG00000037706" "ENSMUSG00000055912" "ENSMUSG00000051839" "ENSMUSG00000019970" "ENSMUSG00000022108"
 [301] "ENSMUSG00000018973" "ENSMUSG00000029394" "ENSMUSG00000006398" "ENSMUSG00000027496" "ENSMUSG00000020571" "ENSMUSG00000020914"
 [307] "ENSMUSG00000039476" "ENSMUSG00000038633" "ENSMUSG00000025889" "ENSMUSG00000031432" "ENSMUSG00000029337" "ENSMUSG00000056612"
 [313] "ENSMUSG00000019478" "ENSMUSG00000034424" "ENSMUSG00000053897" "ENSMUSG00000042770" "ENSMUSG00000075701" "ENSMUSG00000026020"
 [319] "ENSMUSG00000022055" "ENSMUSG00000040158" "ENSMUSG00000027506" "ENSMUSG00000028393" "ENSMUSG00000033831" "ENSMUSG00000062825"
 [325] "ENSMUSG00000003814" "ENSMUSG00000027500" "ENSMUSG00000023944" "ENSMUSG00000085645" "ENSMUSG00000021469" "ENSMUSG00000026497"
 [331] "ENSMUSG00000044927" "ENSMUSG00000026418" "ENSMUSG00000070473" "ENSMUSG00000008348" "ENSMUSG00000054191" "ENSMUSG00000013584"
 [337] "ENSMUSG00000031353" "ENSMUSG00000005873" "ENSMUSG00000028435" "ENSMUSG00000047407" "ENSMUSG00000067367" "ENSMUSG00000032348"
 [343] "ENSMUSG00000005054" "ENSMUSG00000001493" "ENSMUSG00000021520" "ENSMUSG00000062070" "ENSMUSG00000027422" "ENSMUSG00000027210"
 [349] "ENSMUSG00000005575" "ENSMUSG00000028478" "ENSMUSG00000053398" "ENSMUSG00000026473" "ENSMUSG00000026414" "ENSMUSG00000031609"
 [355] "ENSMUSG00000025134" "ENSMUSG00000054766" "ENSMUSG00000001025" "ENSMUSG00000036752" "ENSMUSG00000030538" "ENSMUSG00000046718"
 [361] "ENSMUSG00000033227" "ENSMUSG00000096768" "ENSMUSG00000052727" "ENSMUSG00000038192" "ENSMUSG00000067288" "ENSMUSG00000022490"
 [367] "ENSMUSG00000027082" "ENSMUSG00000032436" "ENSMUSG00000000568" "ENSMUSG00000031586" "ENSMUSG00000053560" "ENSMUSG00000025630"
 [373] "ENSMUSG00000021270" "ENSMUSG00000022528" "ENSMUSG00000032231" "ENSMUSG00000059412" "ENSMUSG00000000958" "ENSMUSG00000027690"
 [379] "ENSMUSG00000025056" "ENSMUSG00000074217" "ENSMUSG00000028195" "ENSMUSG00000028039" "ENSMUSG00000029502" "ENSMUSG00000010095"
 [385] "ENSMUSG00000043866" "ENSMUSG00000024805" "ENSMUSG00000022186" "ENSMUSG00000020388" "ENSMUSG00000002068" "ENSMUSG00000032294"
 [391] "ENSMUSG00000026421" "ENSMUSG00000011179" "ENSMUSG00000032085" "ENSMUSG00000026568" "ENSMUSG00000040726" "ENSMUSG00000042675"
 [397] "ENSMUSG00000022949" "ENSMUSG00000043091" "ENSMUSG00000032575" "ENSMUSG00000063229" "ENSMUSG00000093674" "ENSMUSG00000039131"
 [403] "ENSMUSG00000018500" "ENSMUSG00000048583" "ENSMUSG00000016319" "ENSMUSG00000031548" "ENSMUSG00000027985" "ENSMUSG00000023495"
 [409] "ENSMUSG00000025151" "ENSMUSG00000050708" "ENSMUSG00000026385" "ENSMUSG00000032060" "ENSMUSG00000078713" "ENSMUSG00000055044"
 [415] "ENSMUSG00000066979" "ENSMUSG00000063632" "ENSMUSG00000031661" "ENSMUSG00000006205" "ENSMUSG00000006740" "ENSMUSG00000003436"
 [421] "ENSMUSG00000025270" "ENSMUSG00000078566" "ENSMUSG00000032803" "ENSMUSG00000024644" "ENSMUSG00000035960" "ENSMUSG00000064326"
 [427] "ENSMUSG00000038502" "ENSMUSG00000018102" "ENSMUSG00000022500" "ENSMUSG00000038412" "ENSMUSG00000045330" "ENSMUSG00000027804"
 [433] "ENSMUSG00000046434" "ENSMUSG00000025130" "ENSMUSG00000050621" "ENSMUSG00000060461" "ENSMUSG00000029591" "ENSMUSG00000057666"
 [439] "ENSMUSG00000032299" "ENSMUSG00000038298" "ENSMUSG00000026295" "ENSMUSG00000029752" "ENSMUSG00000034203" "ENSMUSG00000041488"
 [445] "ENSMUSG00000010830" "ENSMUSG00000050953" "ENSMUSG00000032076" "ENSMUSG00000056648" "ENSMUSG00000029538" "ENSMUSG00000035504"
 [451] "ENSMUSG00000062382" "ENSMUSG00000047843" "ENSMUSG00000001657" "ENSMUSG00000021613" "ENSMUSG00000059743" "ENSMUSG00000035585"
 [457] "ENSMUSG00000045377" "ENSMUSG00000028744" "ENSMUSG00000023781" "ENSMUSG00000031162" "ENSMUSG00000032068" "ENSMUSG00000027775"
 [463] "ENSMUSG00000090733" "ENSMUSG00000028946" "ENSMUSG00000061082" "ENSMUSG00000037278" "ENSMUSG00000035021" "ENSMUSG00000067194"
 [469] "ENSMUSG00000032554" "ENSMUSG00000079042" "ENSMUSG00000019139" "ENSMUSG00000058550" "ENSMUSG00000046711" "ENSMUSG00000096145"
 [475] "ENSMUSG00000060743" "ENSMUSG00000079478" "ENSMUSG00000039278" "ENSMUSG00000028640" "ENSMUSG00000025364" "ENSMUSG00000030800"
 [481] "ENSMUSG00000001525" "ENSMUSG00000024868" "ENSMUSG00000027968" "ENSMUSG00000041801" "ENSMUSG00000029328" "ENSMUSG00000022051"
 [487] "ENSMUSG00000030867" "ENSMUSG00000015656" "ENSMUSG00000018567" "ENSMUSG00000062300" "ENSMUSG00000026921" "ENSMUSG00000020307"
 [493] "ENSMUSG00000019528" "ENSMUSG00000003355" "ENSMUSG00000022010" "ENSMUSG00000031734" "ENSMUSG00000021250" "ENSMUSG00000004032"
 [499] "ENSMUSG00000026434" "ENSMUSG00000006390" "ENSMUSG00000042357" "ENSMUSG00000047501" "ENSMUSG00000073940" "ENSMUSG00000021792"
 [505] "ENSMUSG00000037966" "ENSMUSG00000025856" "ENSMUSG00000032320" "ENSMUSG00000019210" "ENSMUSG00000007038" "ENSMUSG00000029322"
 [511] "ENSMUSG00000004771" "ENSMUSG00000071076" "ENSMUSG00000053559" "ENSMUSG00000034484" "ENSMUSG00000024521" "ENSMUSG00000091898"
 [517] "ENSMUSG00000062580" "ENSMUSG00000067818" "ENSMUSG00000001348" "ENSMUSG00000021242" "ENSMUSG00000018698" "ENSMUSG00000028173"
 [523] "ENSMUSG00000031239" "ENSMUSG00000025608" "ENSMUSG00000009248" "ENSMUSG00000052684" "ENSMUSG00000008682" "ENSMUSG00000032221"
 [529] "ENSMUSG00000028266" "ENSMUSG00000038007" "ENSMUSG00000001240" "ENSMUSG00000057863" "ENSMUSG00000030268" "ENSMUSG00000027004"
 [535] "ENSMUSG00000028776" "ENSMUSG00000003161" "ENSMUSG00000028124" "ENSMUSG00000007039" "ENSMUSG00000029843" "ENSMUSG00000040713"
 [541] "ENSMUSG00000033860" "ENSMUSG00000030872" "ENSMUSG00000043445" "ENSMUSG00000020477" "ENSMUSG00000054196" "ENSMUSG00000037712"
 [547] "ENSMUSG00000021848" "ENSMUSG00000086061" "ENSMUSG00000020432" "ENSMUSG00000051176" "ENSMUSG00000044279" "ENSMUSG00000025289"
 [553] "ENSMUSG00000038235" "ENSMUSG00000041841" "ENSMUSG00000061983" "ENSMUSG00000020803" "ENSMUSG00000002233" "ENSMUSG00000006200"
 [559] "ENSMUSG00000026124" "ENSMUSG00000029405" "ENSMUSG00000062867" "ENSMUSG00000023004" "ENSMUSG00000009145" "ENSMUSG00000022961"
 [565] "ENSMUSG00000025732" "ENSMUSG00000025492" "ENSMUSG00000019943" "ENSMUSG00000021377" "ENSMUSG00000016308" "ENSMUSG00000028786"
 [571] "ENSMUSG00000032279" "ENSMUSG00000022136" "ENSMUSG00000028693" "ENSMUSG00000024827" "ENSMUSG00000055612" "ENSMUSG00000040785"
 [577] "ENSMUSG00000023456" "ENSMUSG00000027018" "ENSMUSG00000053644" "ENSMUSG00000033585" "ENSMUSG00000049866" "ENSMUSG00000010608"
 [583] "ENSMUSG00000037266" "ENSMUSG00000027227" "ENSMUSG00000040945" "ENSMUSG00000038936" "ENSMUSG00000029247" "ENSMUSG00000024197"
 [589] "ENSMUSG00000039878" "ENSMUSG00000074637" "ENSMUSG00000028843" "ENSMUSG00000036782" "ENSMUSG00000022464" "ENSMUSG00000020875"
 [595] "ENSMUSG00000018585" "ENSMUSG00000079197" "ENSMUSG00000054422" "ENSMUSG00000025001" "ENSMUSG00000050628" "ENSMUSG00000004642"
 [601] "ENSMUSG00000000326" "ENSMUSG00000003824" "ENSMUSG00000021876" "ENSMUSG00000024997" "ENSMUSG00000020808" "ENSMUSG00000010607"
 [607] "ENSMUSG00000021506" "ENSMUSG00000057836" "ENSMUSG00000020608" "ENSMUSG00000027547" "ENSMUSG00000025980" "ENSMUSG00000019773"
 [613] "ENSMUSG00000028496" "ENSMUSG00000003868" "ENSMUSG00000026520" "ENSMUSG00000018821" "ENSMUSG00000047446" "ENSMUSG00000032898"
 [619] "ENSMUSG00000007739" "ENSMUSG00000066705" "ENSMUSG00000008035" "ENSMUSG00000048528" "ENSMUSG00000026701" "ENSMUSG00000027342"
 [625] "ENSMUSG00000027306" "ENSMUSG00000023045" "ENSMUSG00000031073" "ENSMUSG00000056501" "ENSMUSG00000031897" "ENSMUSG00000042821"
 [631] "ENSMUSG00000021493" "ENSMUSG00000045690" "ENSMUSG00000000690" "ENSMUSG00000000078" "ENSMUSG00000071547" "ENSMUSG00000043439"
 [637] "ENSMUSG00000005413" "ENSMUSG00000063445" "ENSMUSG00000023942" "ENSMUSG00000068522" "ENSMUSG00000041012" "ENSMUSG00000067924"
 [643] "ENSMUSG00000022255" "ENSMUSG00000027203" "ENSMUSG00000036111" "ENSMUSG00000039985" "ENSMUSG00000090841" "ENSMUSG00000030970"
 [649] "ENSMUSG00000022336" "ENSMUSG00000071658" "ENSMUSG00000021474" "ENSMUSG00000034675" "ENSMUSG00000001418" "ENSMUSG00000062248"
 [655] "ENSMUSG00000057322" "ENSMUSG00000028228" "ENSMUSG00000027248" "ENSMUSG00000023905" "ENSMUSG00000030688" "ENSMUSG00000055850"
 [661] "ENSMUSG00000030695" "ENSMUSG00000028717" "ENSMUSG00000006005" "ENSMUSG00000030417" "ENSMUSG00000045136" "ENSMUSG00000052837"
 [667] "ENSMUSG00000020077" "ENSMUSG00000050212" "ENSMUSG00000024588" "ENSMUSG00000029177" "ENSMUSG00000055436" "ENSMUSG00000019437"
 [673] "ENSMUSG00000023092" "ENSMUSG00000034205" "ENSMUSG00000060572" "ENSMUSG00000011752" "ENSMUSG00000022474" "ENSMUSG00000096546"
 [679] "ENSMUSG00000073599" "ENSMUSG00000027078" "ENSMUSG00000041355" "ENSMUSG00000020029" "ENSMUSG00000031170" "ENSMUSG00000021290"
 [685] "ENSMUSG00000008859" "ENSMUSG00000055148" "ENSMUSG00000016382" "ENSMUSG00000031160" "ENSMUSG00000001056" "ENSMUSG00000044303"
 [691] "ENSMUSG00000025232" "ENSMUSG00000043004" "ENSMUSG00000020863" "ENSMUSG00000027170" "ENSMUSG00000025511" "ENSMUSG00000020458"
 [697] "ENSMUSG00000020897" "ENSMUSG00000042462" "ENSMUSG00000005566" "ENSMUSG00000033998" "ENSMUSG00000019432" "ENSMUSG00000039001"
 [703] "ENSMUSG00000064264" "ENSMUSG00000074748" "ENSMUSG00000018659" "ENSMUSG00000057113" "ENSMUSG00000019960" "ENSMUSG00000032324"
 [709] "ENSMUSG00000034892" "ENSMUSG00000031447" "ENSMUSG00000002997" "ENSMUSG00000003380" "ENSMUSG00000054871" "ENSMUSG00000027405"
 [715] "ENSMUSG00000029623" "ENSMUSG00000005233" "ENSMUSG00000052102" "ENSMUSG00000027495" "ENSMUSG00000020935" "ENSMUSG00000041688"
 [721] "ENSMUSG00000048373" "ENSMUSG00000059708" "ENSMUSG00000036438" "ENSMUSG00000029802" "ENSMUSG00000025035" "ENSMUSG00000032081"
 [727] "ENSMUSG00000073243" "ENSMUSG00000032679" "ENSMUSG00000046942" "ENSMUSG00000015575" "ENSMUSG00000020484" "ENSMUSG00000020321"
 [733] "ENSMUSG00000033863" "ENSMUSG00000024856" "ENSMUSG00000046516" "ENSMUSG00000060152" "ENSMUSG00000024646" "ENSMUSG00000044894"
 [739] "ENSMUSG00000028743" "ENSMUSG00000031502" "ENSMUSG00000042797" "ENSMUSG00000030747" "ENSMUSG00000032216" "ENSMUSG00000027559"
 [745] "ENSMUSG00000028023" "ENSMUSG00000025499" "ENSMUSG00000010797" "ENSMUSG00000024772" "ENSMUSG00000044461" "ENSMUSG00000031604"
 [751] "ENSMUSG00000040459" "ENSMUSG00000025268" "ENSMUSG00000016386" "ENSMUSG00000031403" "ENSMUSG00000015579" "ENSMUSG00000025381"
 [757] "ENSMUSG00000046330" "ENSMUSG00000031068" "ENSMUSG00000031229" "ENSMUSG00000001089" "ENSMUSG00000029614" "ENSMUSG00000029641"
 [763] "ENSMUSG00000045667" "ENSMUSG00000007892" "ENSMUSG00000032492" "ENSMUSG00000020089" "ENSMUSG00000024986" "ENSMUSG00000055723"
 [769] "ENSMUSG00000028494" "ENSMUSG00000098178" "ENSMUSG00000028158" "ENSMUSG00000036446" "ENSMUSG00000035376" "ENSMUSG00000032383"
 [775] "ENSMUSG00000060600" "ENSMUSG00000024014" "ENSMUSG00000048752" "ENSMUSG00000070544" "ENSMUSG00000052957" "ENSMUSG00000026202"
 [781] "ENSMUSG00000024907" "ENSMUSG00000018822" "ENSMUSG00000021484" "ENSMUSG00000031708" "ENSMUSG00000072949" "ENSMUSG00000038236"
 [787] "ENSMUSG00000024991" "ENSMUSG00000019579" "ENSMUSG00000062380" "ENSMUSG00000045328" "ENSMUSG00000022180" "ENSMUSG00000023067"
 [793] "ENSMUSG00000024177" "ENSMUSG00000047613" "ENSMUSG00000040666" "ENSMUSG00000053253" "ENSMUSG00000036390" "ENSMUSG00000008393"
 [799] "ENSMUSG00000037070" "ENSMUSG00000059741" "ENSMUSG00000027160" "ENSMUSG00000021095" "ENSMUSG00000031217" "ENSMUSG00000004610"
 [805] "ENSMUSG00000021131" "ENSMUSG00000021576" "ENSMUSG00000044408" "ENSMUSG00000066456" "ENSMUSG00000028949" "ENSMUSG00000028034"
 [811] "ENSMUSG00000003559" "ENSMUSG00000037740" "ENSMUSG00000013415" "ENSMUSG00000037025" "ENSMUSG00000000385" "ENSMUSG00000063065"
 [817] "ENSMUSG00000035041" "ENSMUSG00000036139" "ENSMUSG00000005973" "ENSMUSG00000096356" "ENSMUSG00000048007" "ENSMUSG00000008601"
 [823] "ENSMUSG00000030189" "ENSMUSG00000037166" "ENSMUSG00000038943" "ENSMUSG00000020108" "ENSMUSG00000021466" "ENSMUSG00000017861"
 [829] "ENSMUSG00000060860" "ENSMUSG00000024640" "ENSMUSG00000046714" "ENSMUSG00000053907" "ENSMUSG00000020483" "ENSMUSG00000015335"
 [835] "ENSMUSG00000000730" "ENSMUSG00000039103" "ENSMUSG00000067925" "ENSMUSG00000022247" "ENSMUSG00000074457" "ENSMUSG00000028889"
 [841] "ENSMUSG00000020176" "ENSMUSG00000028480" "ENSMUSG00000028138" "ENSMUSG00000015932" "ENSMUSG00000052854" "ENSMUSG00000024190"
 [847] "ENSMUSG00000017760" "ENSMUSG00000034868" "ENSMUSG00000037742" "ENSMUSG00000044338" "ENSMUSG00000062929" "ENSMUSG00000031387"
 [853] "ENSMUSG00000032766" "ENSMUSG00000030127" "ENSMUSG00000038668" "ENSMUSG00000090137" "ENSMUSG00000030587" "ENSMUSG00000050966"
 [859] "ENSMUSG00000030541" "ENSMUSG00000047261" "ENSMUSG00000039956" "ENSMUSG00000025494" "ENSMUSG00000059552" "ENSMUSG00000030699"
 [865] "ENSMUSG00000025613" "ENSMUSG00000063870" "ENSMUSG00000024012" "ENSMUSG00000024803" "ENSMUSG00000038227" "ENSMUSG00000047126"
 [871] "ENSMUSG00000029064" "ENSMUSG00000042757" "ENSMUSG00000049969" "ENSMUSG00000078784" "ENSMUSG00000032369" "ENSMUSG00000005583"
 [877] "ENSMUSG00000026664" "ENSMUSG00000073481" "ENSMUSG00000020078" "ENSMUSG00000045503" "ENSMUSG00000063972" "ENSMUSG00000034875"
 [883] "ENSMUSG00000026817" "ENSMUSG00000062960" "ENSMUSG00000057278" "ENSMUSG00000005836" "ENSMUSG00000030844" "ENSMUSG00000026956"
 [889] "ENSMUSG00000038009" "ENSMUSG00000036427" "ENSMUSG00000031737" "ENSMUSG00000022415" "ENSMUSG00000026678" "ENSMUSG00000059246"
 [895] "ENSMUSG00000001247" "ENSMUSG00000026278" "ENSMUSG00000054428" "ENSMUSG00000093904" "ENSMUSG00000039886" "ENSMUSG00000030492"
 [901] "ENSMUSG00000041571" "ENSMUSG00000038695" "ENSMUSG00000023272" "ENSMUSG00000002580" "ENSMUSG00000024725" "ENSMUSG00000061787"
 [907] "ENSMUSG00000006369" "ENSMUSG00000000253" "ENSMUSG00000022587" "ENSMUSG00000039176" "ENSMUSG00000058258" "ENSMUSG00000059534"
 [913] "ENSMUSG00000061353" "ENSMUSG00000046841" "ENSMUSG00000029616" "ENSMUSG00000020163" "ENSMUSG00000005354" "ENSMUSG00000026234"
 [919] "ENSMUSG00000006360" "ENSMUSG00000035551" "ENSMUSG00000055296" "ENSMUSG00000036241" "ENSMUSG00000029007" "ENSMUSG00000038388"
 [925] "ENSMUSG00000069833" "ENSMUSG00000034845" "ENSMUSG00000050288" "ENSMUSG00000074682" "ENSMUSG00000021149" "ENSMUSG00000109644"
 [931] "ENSMUSG00000061393" "ENSMUSG00000032014" "ENSMUSG00000042448" "ENSMUSG00000061186" "ENSMUSG00000034285" "ENSMUSG00000003585"
 [937] "ENSMUSG00000005667" "ENSMUSG00000028943" "ENSMUSG00000037161" "ENSMUSG00000029344" "ENSMUSG00000022101" "ENSMUSG00000019539"
 [943] "ENSMUSG00000028684" "ENSMUSG00000034880" "ENSMUSG00000055943" "ENSMUSG00000020248" "ENSMUSG00000042607" "ENSMUSG00000037062"
 [949] "ENSMUSG00000031990" "ENSMUSG00000017009" "ENSMUSG00000079184" "ENSMUSG00000025982" "ENSMUSG00000004631" "ENSMUSG00000020277"
 [955] "ENSMUSG00000000278" "ENSMUSG00000025190" "ENSMUSG00000073400" "ENSMUSG00000035000" "ENSMUSG00000087658" "ENSMUSG00000031917"
 [961] "ENSMUSG00000071528" "ENSMUSG00000051154" "ENSMUSG00000034248" "ENSMUSG00000037960" "ENSMUSG00000020570" "ENSMUSG00000025196"
 [967] "ENSMUSG00000078249" "ENSMUSG00000022816" "ENSMUSG00000028040" "ENSMUSG00000025880" "ENSMUSG00000025260" "ENSMUSG00000011884"
 [973] "ENSMUSG00000026185" "ENSMUSG00000008540" "ENSMUSG00000008450" "ENSMUSG00000028675" "ENSMUSG00000024409" "ENSMUSG00000028011"
 [979] "ENSMUSG00000050105" "ENSMUSG00000038580" "ENSMUSG00000068882" "ENSMUSG00000028567" "ENSMUSG00000072115" "ENSMUSG00000022382"
 [985] "ENSMUSG00000024446" "ENSMUSG00000028800" "ENSMUSG00000073125" "ENSMUSG00000021814" "ENSMUSG00000068048" "ENSMUSG00000047721"
 [991] "ENSMUSG00000021850" "ENSMUSG00000041378" "ENSMUSG00000090523" "ENSMUSG00000036523" "ENSMUSG00000025283" "ENSMUSG00000006235"
 [997] "ENSMUSG00000023443" "ENSMUSG00000021458" "ENSMUSG00000030470" "ENSMUSG00000059895"
 [ reached getOption("max.print") -- omitted 4000 entries ]

Build KNN graphs

For corrected and uncorrected data

embryo_milo_uncor <- buildGraph(embryo_milo_uncor, k = 30, d=30, seed=42)

Constructing kNN graph with k:30

scater::plotReducedDim(embryo_milo_uncor, dimred = "UMAP", colour_by = "sequencing.batch")

scater::plotReducedDim(embryo_milo_mnn, dimred = "umap", colour_by = "sequencing.batch")

scater::plotReducedDim(embryo_milo_uncor, dimred = "UMAP", colour_by = "pool")

scater::plotReducedDim(embryo_milo_mnn, dimred = "umap", colour_by = "pool")

Make neighbourhoods

embryo_milo_uncor <- countCells(embryo_milo_uncor, meta.data = data.frame(colData(embryo_milo_uncor)), sample="sample")

Checking meta.data validity
Setting up matrix with 11895 neighbourhoods
Counting cells in neighbourhoods

\

Error: unexpected input in "\"

Make design matrix

embryo_milo_mnn <- calcNhoodDistance(embryo_milo_mnn, d=30, reduced.dim = "PCA")
embryo_milo_uncor <- calcNhoodDistance(embryo_milo_uncor, d=30, reduced.dim = "PCA")

Try doing DA analysis with or without including the technical covariate in the design

da_uncor_stage_batch <- testNhoods(embryo_milo_uncor, design = ~ sequencing.batch + stage_int, design.df = embryo_design)

Performing spatial FDR correction withk-distance weightingPerforming spatial FDR correction withneighbour-distance weightingPerforming spatial FDR correction withedge weightingPerforming spatial FDR correction withvertex weightingPerforming spatial FDR correction withnone weighting

Diagnostic plots

ggplot(da_mnn_stage, aes(SpatialFDR)) + geom_histogram() +
ggplot(da_mnn_stage, aes(logFC, -log10(SpatialFDR))) + geom_point()

ggplot(da_mnn_stage_batch, aes(SpatialFDR)) + geom_histogram() +
ggplot(da_mnn_stage_batch, aes(logFC, -log10(SpatialFDR))) +
  geom_point()

ggplot(da_uncor_stage, aes(SpatialFDR)) + geom_histogram() +
ggplot(da_uncor_stage, aes(logFC, -log10(SpatialFDR))) +
  geom_point()

ggplot(da_uncor_stage_batch, aes(SpatialFDR)) + geom_histogram() +
ggplot(da_uncor_stage_batch, aes(logFC, -log10(SpatialFDR))) +
  geom_point()

NA
NA

bind_rows(mutate(da_mnn_stage, design="stage", correction="MNN"),

Warning messages:
1: In readChar(file, size, TRUE) : truncating string with embedded nuls
2: In readChar(file, size, TRUE) : truncating string with embedded nuls
3: In readChar(file, size, TRUE) : truncating string with embedded nuls
4: In readChar(file, size, TRUE) : truncating string with embedded nuls
5: In readChar(file, size, TRUE) : truncating string with embedded nuls
6: In readChar(file, size, TRUE) : truncating string with embedded nuls
7: In readChar(file, size, TRUE) : truncating string with embedded nuls
8: In readChar(file, size, TRUE) : truncating string with embedded nuls

          mutate(da_mnn_stage_batch, design="stage_batch", correction="MNN"),
          mutate(da_uncor_stage, design="stage", correction="uncor"),
          mutate(da_uncor_stage_batch, design="stage_batch", correction="uncor"),
          ) %>%
  mutate(is_signif=SpatialFDR < 0.01) %>%
  mutate(class=paste(correction, design)) %>%
    ggplot(aes(class, fill=is_signif)) +
    geom_bar(position="fill")

Save objects

saveRDS(embryo_milo_mnn, "~/EmbryoAtlas_MNN_milo.RDS")

Warning messages:
1: In readChar(file, size, TRUE) : truncating string with embedded nuls
2: In readChar(file, size, TRUE) : truncating string with embedded nuls
3: In readChar(file, size, TRUE) : truncating string with embedded nuls
4: In readChar(file, size, TRUE) : truncating string with embedded nuls
5: In readChar(file, size, TRUE) : truncating string with embedded nuls
6: In readChar(file, size, TRUE) : truncating string with embedded nuls
7: In readChar(file, size, TRUE) : truncating string with embedded nuls
8: In readChar(file, size, TRUE) : truncating string with embedded nuls

Visualize DA neighbourhoods

embryo_milo_mnn <- buildNhoodGraph(embryo_milo_mnn)